A biokinematic approach for the computational simulation of proteins molecular mechanism

Proteins play an essential role in the biological processes that take place in the human body. For this reason, it is very important to understand the molecular mechanisms involved. Recently a new approach, based on the parallelism between proteins and spatial mechanisms, has allowed methods to be developed to obtain atomic trajectories for protein motion using concepts from the kinematics of mechanisms. This paper presents a method for simulating protein motion, based on the evaluation of the potential energy during the motion, thereby avoiding the need to perform a minimization procedure. This approach constitutes a good compromise between computational effort and accuracy of the results. In addition, in order to efficiently simulate the motion, a new algorithm for normalization of the structure of the protein is presented. Finally, we illustrate the results of applying this method to an inorganic pyrophosphatase (family II) from Streptococcus gordonii evaluating geometric accuracy, energetic evolution and biological indicators.

► The paper presents a method for simulating protein motion, using potential energy feedback. ► A new algorithm for normalization of the structure of the protein is presented. ► The approach constitutes a good compromise between computational effort and accuracy.